SummaryThe project outlined here addresses the fundamental question how the brain encodes and controls behavior. While we have a reasonable understanding of the role of entire brain areas in such processes, and of mechanisms at the molecular and synaptic levels, there is a big gap in our knowledge of how behavior is controlled at the level of defined neuronal circuits.
In natural environments, chances for survival depend on learning about possible aversive and appetitive outcomes and on the appropriate behavioral responses. Most studies addressing the underlying mechanisms at the level of neuronal circuits have focused on aversive learning, such as in Pavlovian fear conditioning. Understanding how activity in defined neuronal circuits mediates appetitive learning, as well as how these circuitries are shared and interact with aversive learning circuits, is a central question in the neuroscience of learning and memory and the focus of this grant application.
Using a multidisciplinary approach in mice, combining behavioral, in vivo and in vitro electrophysiological, imaging, optogenetic and state-of-the-art viral circuit tracing techniques, we aim at dissecting the neuronal circuitry of appetitive Pavlovian conditioning with a focus on the amygdala, a key brain region important for both aversive and appetitive learning. Ultimately, elucidating these mechanisms at the level of defined neurons and circuits is fundamental not only for an understanding of memory processes in the brain in general, but also to inform a mechanistic approach to psychiatric conditions associated with amygdala dysfunction and dysregulated emotional responses including anxiety and mood disorders.

The project outlined here addresses the fundamental question how the brain encodes and controls behavior. While we have a reasonable understanding of the role of entire brain areas in such processes, and of mechanisms at the molecular and synaptic levels, there is a big gap in our knowledge of how behavior is controlled at the level of defined neuronal circuits.
In natural environments, chances for survival depend on learning about possible aversive and appetitive outcomes and on the appropriate behavioral responses. Most studies addressing the underlying mechanisms at the level of neuronal circuits have focused on aversive learning, such as in Pavlovian fear conditioning. Understanding how activity in defined neuronal circuits mediates appetitive learning, as well as how these circuitries are shared and interact with aversive learning circuits, is a central question in the neuroscience of learning and memory and the focus of this grant application.
Using a multidisciplinary approach in mice, combining behavioral, in vivo and in vitro electrophysiological, imaging, optogenetic and state-of-the-art viral circuit tracing techniques, we aim at dissecting the neuronal circuitry of appetitive Pavlovian conditioning with a focus on the amygdala, a key brain region important for both aversive and appetitive learning. Ultimately, elucidating these mechanisms at the level of defined neurons and circuits is fundamental not only for an understanding of memory processes in the brain in general, but also to inform a mechanistic approach to psychiatric conditions associated with amygdala dysfunction and dysregulated emotional responses including anxiety and mood disorders.

SummaryCalcium-activated chloride channels (CaCCs) play key roles in a range of physiological processes such as the control of membrane excitability, photoreception and epithelial secretion. Although the importance of these channels has been recognized for more than 30 years their molecular identity remained obscure. The recent discovery of two protein families encoding for CaCCs, Anoctamins and Bestrophins, was a scientific breakthrough that has provided first insight into two novel ion channel architectures. Within this proposal we aim to determine the first high resolution structures of members of both families and study their functional behavior by an interdisciplinary approach combining biochemistry, X-ray crystallography and electrophysiology. The structural investigation of eukaryotic membrane proteins is extremely challenging and will require us to investigate large numbers of candidates to single out family members with superior biochemical properties. During the last year we have made large progress in this direction. By screening numerous eukaryotic Anoctamins and prokaryotic Bestrophins we have identified well-behaved proteins for both families, which were successfully scaled-up and purified. Additional family members will be identified within the course of the project. For these stable proteins we plan to grow crystals diffracting to high resolution and to proceed with structure determination. With first structural information in hand we will perform detailed functional studies using electrophysiology and complementary biophysical techniques to gain mechanistic insight into ion permeation and gating. As the pharmacology of both families is still in its infancy we will in later stages also engage in the identification and characterization of inhibitors and activators of Anoctamins and Bestrophins to open up a field that may ultimately lead to the discovery of novel therapeutic strategies targeting calcium-activated chloride channels.

Calcium-activated chloride channels (CaCCs) play key roles in a range of physiological processes such as the control of membrane excitability, photoreception and epithelial secretion. Although the importance of these channels has been recognized for more than 30 years their molecular identity remained obscure. The recent discovery of two protein families encoding for CaCCs, Anoctamins and Bestrophins, was a scientific breakthrough that has provided first insight into two novel ion channel architectures. Within this proposal we aim to determine the first high resolution structures of members of both families and study their functional behavior by an interdisciplinary approach combining biochemistry, X-ray crystallography and electrophysiology. The structural investigation of eukaryotic membrane proteins is extremely challenging and will require us to investigate large numbers of candidates to single out family members with superior biochemical properties. During the last year we have made large progress in this direction. By screening numerous eukaryotic Anoctamins and prokaryotic Bestrophins we have identified well-behaved proteins for both families, which were successfully scaled-up and purified. Additional family members will be identified within the course of the project. For these stable proteins we plan to grow crystals diffracting to high resolution and to proceed with structure determination. With first structural information in hand we will perform detailed functional studies using electrophysiology and complementary biophysical techniques to gain mechanistic insight into ion permeation and gating. As the pharmacology of both families is still in its infancy we will in later stages also engage in the identification and characterization of inhibitors and activators of Anoctamins and Bestrophins to open up a field that may ultimately lead to the discovery of novel therapeutic strategies targeting calcium-activated chloride channels.

Max ERC Funding

2 176 000 €

Duration

Start date: 2014-02-01, End date: 2020-01-31

Project acronymastromnesis

ProjectThe language of astrocytes: multilevel analysis to understand astrocyte communication and its role in memory-related brain operations and in cognitive behavior

Researcher (PI)Andrea Volterra

Host Institution (HI)UNIVERSITE DE LAUSANNE

Call DetailsAdvanced Grant (AdG), LS5, ERC-2013-ADG

SummaryIn the 90s, two landmark observations brought to a paradigm shift about the role of astrocytes in brain function: 1) astrocytes respond to signals coming from other cells with transient Ca2+ elevations; 2) Ca2+ transients in astrocytes trigger release of neuroactive and vasoactive agents. Since then, many modulatory astrocytic actions and mechanisms were described, forming a complex - partly contradictory - picture, in which the exact roles and modes of astrocyte action remain ill defined. Our project wants to bring light into the “language of astrocytes”, i.e. into how they communicate with neurons and, ultimately, address their role in brain computations and cognitive behavior. To this end we will perform 4 complementary levels of analysis using highly innovative methodologies in order to obtain unprecedented results. We will study: 1) the subcellular organization of astrocytes underlying local microdomain communications by use of correlative light-electron microscopy; 2) the way individual astrocytes integrate inputs and control synaptic ensembles using 3D two-photon imaging, genetically-encoded Ca2+ indicators, optogenetics and electrophysiology; 3) the contribution of astrocyte ensembles to behavior-relevant circuit operations using miniaturized microscopes capturing neuronal/astrocytic population dynamics in freely-moving mice during memory tests; 4) the contribution of astrocytic signalling mechanisms to cognitive behavior using a set of new mouse lines with conditional, astrocyte-specific genetic modification of signalling pathways. We expect that this combination of groundbreaking ideas, innovative technologies and multilevel analysis makes our project highly attractive to the neuroscience community at large, bridging aspects of molecular, cellular, systems and behavioral neuroscience, with the goal of leading from a provocative hypothesis to the conclusive demonstration of whether and how “the language of astrocytes” participates in memory and cognition.

In the 90s, two landmark observations brought to a paradigm shift about the role of astrocytes in brain function: 1) astrocytes respond to signals coming from other cells with transient Ca2+ elevations; 2) Ca2+ transients in astrocytes trigger release of neuroactive and vasoactive agents. Since then, many modulatory astrocytic actions and mechanisms were described, forming a complex - partly contradictory - picture, in which the exact roles and modes of astrocyte action remain ill defined. Our project wants to bring light into the “language of astrocytes”, i.e. into how they communicate with neurons and, ultimately, address their role in brain computations and cognitive behavior. To this end we will perform 4 complementary levels of analysis using highly innovative methodologies in order to obtain unprecedented results. We will study: 1) the subcellular organization of astrocytes underlying local microdomain communications by use of correlative light-electron microscopy; 2) the way individual astrocytes integrate inputs and control synaptic ensembles using 3D two-photon imaging, genetically-encoded Ca2+ indicators, optogenetics and electrophysiology; 3) the contribution of astrocyte ensembles to behavior-relevant circuit operations using miniaturized microscopes capturing neuronal/astrocytic population dynamics in freely-moving mice during memory tests; 4) the contribution of astrocytic signalling mechanisms to cognitive behavior using a set of new mouse lines with conditional, astrocyte-specific genetic modification of signalling pathways. We expect that this combination of groundbreaking ideas, innovative technologies and multilevel analysis makes our project highly attractive to the neuroscience community at large, bridging aspects of molecular, cellular, systems and behavioral neuroscience, with the goal of leading from a provocative hypothesis to the conclusive demonstration of whether and how “the language of astrocytes” participates in memory and cognition.

Max ERC Funding

2 513 896 €

Duration

Start date: 2014-02-01, End date: 2019-01-31

Project acronymBRAINCOMPATH

ProjectMesoscale Brain Dynamics: Computing with Neuronal Pathways

Researcher (PI)Fritjof Helmchen

Host Institution (HI)UNIVERSITAT ZURICH

Call DetailsAdvanced Grant (AdG), LS5, ERC-2014-ADG

SummaryBrain computations rely on proper signal flow through the complex network of connected brain regions. Despite a wealth of anatomical and functional data – from microscopic to macroscopic scale – we still poorly understand the principles of how signal flow is routed through neuronal networks to generate appropriate behavior. Brain dynamics on the 'mesoscopic' scale, the intermediate level where local microcircuits communicate via axonal pathways, has remained a particular blind spot of research as it has been difficult to access under in vivo conditions. Here, I propose to tackle the mesoscopic level of brain dynamics both experimentally and theoretically, adopting a fresh perspective centered on neuronal pathway dynamics. Experimentally, we will utilize and further advance state-of-the-art genetic and optical techniques to create a toolbox for measuring and manipulating signal flow in pathway networks across a broad range of temporal scales. In particular, we will improve fiber-optic based methods for probing the activity of either individual or multiple neuronal pathways with high specificity. Using these tools we will set out to reveal mesoscopic brain dynamics across relevant cortical and subcortical regions in awake, behaving mice. Specifically, we will investigate sensorimotor learning for a reward-based texture discrimination task and rapid sensorimotor control during skilled locomotion. Moreover, by combining fiber-optic methods with two-photon microscopy and fMRI, respectively, we will start linking the meso-level to the micro- and macro-levels. Throughout the project, experiments will be complemented by computational approaches to analyse data, model pathway dynamics, and conceptualize a formal theory of mesoscopic dynamics. This project may transform the field by bridging the hierarchical brain levels and opening significant new avenues to assess physiological as well as pathological signal flow in the brain.

Brain computations rely on proper signal flow through the complex network of connected brain regions. Despite a wealth of anatomical and functional data – from microscopic to macroscopic scale – we still poorly understand the principles of how signal flow is routed through neuronal networks to generate appropriate behavior. Brain dynamics on the 'mesoscopic' scale, the intermediate level where local microcircuits communicate via axonal pathways, has remained a particular blind spot of research as it has been difficult to access under in vivo conditions. Here, I propose to tackle the mesoscopic level of brain dynamics both experimentally and theoretically, adopting a fresh perspective centered on neuronal pathway dynamics. Experimentally, we will utilize and further advance state-of-the-art genetic and optical techniques to create a toolbox for measuring and manipulating signal flow in pathway networks across a broad range of temporal scales. In particular, we will improve fiber-optic based methods for probing the activity of either individual or multiple neuronal pathways with high specificity. Using these tools we will set out to reveal mesoscopic brain dynamics across relevant cortical and subcortical regions in awake, behaving mice. Specifically, we will investigate sensorimotor learning for a reward-based texture discrimination task and rapid sensorimotor control during skilled locomotion. Moreover, by combining fiber-optic methods with two-photon microscopy and fMRI, respectively, we will start linking the meso-level to the micro- and macro-levels. Throughout the project, experiments will be complemented by computational approaches to analyse data, model pathway dynamics, and conceptualize a formal theory of mesoscopic dynamics. This project may transform the field by bridging the hierarchical brain levels and opening significant new avenues to assess physiological as well as pathological signal flow in the brain.

Summary"In recent years, we have made significant contributions to the understanding of the tumour suppressors p53, p16INK4a, and ARF, particularly in relation with cellular senescence and aging. The current project is motivated by two hypothesis: 1) that the INK4/ARF locus is a sensor of epigenetic damage and this is at the basis of its activation by oncogenes and aging; and, 2) that the accumulation of cellular damage and stress is at the basis of both cancer and aging, and consequently ""anti-damage genes"", such as tumour suppressors, simultaneously counteract both cancer and aging. With regard to the INK4/ARF locus, the project includes: 1.1) the generation of null mice for the Regulatory Domain (RD) thought to be essential for the proper regulation of the locus; 1.2) the study of the INK4/ARF anti-sense transcription and its importance for the assembly of Polycomb repressive complexes; 1.3) the generation of mice carrying the human INK4/ARF locus to analyze, among other aspects, whether the known differences between the human and murine loci are ""locus autonomous""; and, 1.4) to analyze the INK4/ARF locus in the process of epigenetic reprogramming both from ES cells to differentiated cells and, conversely, from differentiated cells to induced-pluripotent stem (iPS) cells. With regard to the impact of ""anti-damage genes"" on cancer and aging, the project includes: 2.1) the analysis of the aging of super-INK4/ARF mice and super-p53 mice; 2.2) we have generated super-PTEN mice and we will examine whether PTEN not only confers cancer resistance but also anti-aging activity; and, finally, 2.3) we have generated super-SIRT1 mice, which is among the best-characterized anti-aging genes in non-mammalian model systems (where it is named Sir2) involved in protection from metabolic damage, and we will study the cancer and aging of these mice. Together, this project will significantly advance our understanding of the molecular mechanisms underlying cancer and aging."

"In recent years, we have made significant contributions to the understanding of the tumour suppressors p53, p16INK4a, and ARF, particularly in relation with cellular senescence and aging. The current project is motivated by two hypothesis: 1) that the INK4/ARF locus is a sensor of epigenetic damage and this is at the basis of its activation by oncogenes and aging; and, 2) that the accumulation of cellular damage and stress is at the basis of both cancer and aging, and consequently ""anti-damage genes"", such as tumour suppressors, simultaneously counteract both cancer and aging. With regard to the INK4/ARF locus, the project includes: 1.1) the generation of null mice for the Regulatory Domain (RD) thought to be essential for the proper regulation of the locus; 1.2) the study of the INK4/ARF anti-sense transcription and its importance for the assembly of Polycomb repressive complexes; 1.3) the generation of mice carrying the human INK4/ARF locus to analyze, among other aspects, whether the known differences between the human and murine loci are ""locus autonomous""; and, 1.4) to analyze the INK4/ARF locus in the process of epigenetic reprogramming both from ES cells to differentiated cells and, conversely, from differentiated cells to induced-pluripotent stem (iPS) cells. With regard to the impact of ""anti-damage genes"" on cancer and aging, the project includes: 2.1) the analysis of the aging of super-INK4/ARF mice and super-p53 mice; 2.2) we have generated super-PTEN mice and we will examine whether PTEN not only confers cancer resistance but also anti-aging activity; and, finally, 2.3) we have generated super-SIRT1 mice, which is among the best-characterized anti-aging genes in non-mammalian model systems (where it is named Sir2) involved in protection from metabolic damage, and we will study the cancer and aging of these mice. Together, this project will significantly advance our understanding of the molecular mechanisms underlying cancer and aging."

Max ERC Funding

2 000 000 €

Duration

Start date: 2009-04-01, End date: 2015-03-31

Project acronymCCICO

ProjectCoupled and Competing Instabilities in Complex Oxides

Researcher (PI)Nicola Ann Spaldin

Host Institution (HI)EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Call DetailsAdvanced Grant (AdG), PE3, ERC-2011-ADG_20110209

Summary"The CCICO project will build a comprehensive understanding of how proximity to previously unexplored combinations of instabilities, as well as previously unidentified types of ordering, manifest in novel behaviors, and will develop design guidelines for practical realization of new materials with such behaviors. Taking transition-metal oxides as our model systems, we will develop and apply first-principles electronic structure theory methods to explore an extensive array of new combinations of orderings, with a focus on interactions between the electronic -- Jahn-Teller, orbital and charge -- and structural -- rotations, ferroelectric and other distortions -- degrees of freedom. Our goal is to spawn a new field of study based on a novel combination of orderings in the same way that the field of multiferroics was jump-started ten years ago by our work understanding the coexistence of ferroelectricity and magnetism. Conversely, we will apply the computational tools developed in our history of studying multiferroics, particularly descriptions of proximity to structural and magnetic phase transitions, to characterizing observed behaviors such as exotic superconductivity in existing materials. In the process we will search for and characterize elusive or poorly characterized forms of order in solids, with a focus on ferrotoroidicity and emergent local dipoles. A final application is to create designer materials for solid-state experiments relevant to high-energy physics and cosmology. Promising compounds that are amenable to bulk synthesis will be made in our new oxide single-crystal growth laboratory; materials that require thin-film routes will be pursued in collaboration with colleagues."

"The CCICO project will build a comprehensive understanding of how proximity to previously unexplored combinations of instabilities, as well as previously unidentified types of ordering, manifest in novel behaviors, and will develop design guidelines for practical realization of new materials with such behaviors. Taking transition-metal oxides as our model systems, we will develop and apply first-principles electronic structure theory methods to explore an extensive array of new combinations of orderings, with a focus on interactions between the electronic -- Jahn-Teller, orbital and charge -- and structural -- rotations, ferroelectric and other distortions -- degrees of freedom. Our goal is to spawn a new field of study based on a novel combination of orderings in the same way that the field of multiferroics was jump-started ten years ago by our work understanding the coexistence of ferroelectricity and magnetism. Conversely, we will apply the computational tools developed in our history of studying multiferroics, particularly descriptions of proximity to structural and magnetic phase transitions, to characterizing observed behaviors such as exotic superconductivity in existing materials. In the process we will search for and characterize elusive or poorly characterized forms of order in solids, with a focus on ferrotoroidicity and emergent local dipoles. A final application is to create designer materials for solid-state experiments relevant to high-energy physics and cosmology. Promising compounds that are amenable to bulk synthesis will be made in our new oxide single-crystal growth laboratory; materials that require thin-film routes will be pursued in collaboration with colleagues."

Max ERC Funding

2 000 000 €

Duration

Start date: 2012-03-01, End date: 2017-02-28

Project acronymCEMAS

ProjectControlling and Exploring Molecular Systems at the Atomic Scale with Atomic Force Microscopy

Researcher (PI)Gerhard Meyer

Host Institution (HI)IBM RESEARCH GMBH

Call DetailsAdvanced Grant (AdG), PE3, ERC-2011-ADG_20110209

SummaryThe objective of this project is to advance and use Atomic Force Microscopy (AFM) to explore the physical and chemical properties of single molecules and molecular systems with unprecedented spatial resolution. We will use AFM to develop atomically resolved molecular imaging with structural and chemical identification and investigate charge distribution and transfer in molecular systems. The AFM will allow the extension of seminal Scanning Tunneling Microscopy (STM) work on atoms/molecules on ultra-thin insulating films to thick insulating films, to control and explore single molecule chemistry processes in utmost detail. The whole work will be significantly based on the development and exploitation of novel atomic and molecular manipulation processes to control matter at the atomic scale, both for fabricating novel complex molecular nanostructures with atomic scale precision and understanding these systems, as well as for probe-tip functionalization to tailor tip-substrate interaction. Instrumental enhancements will focus on fabricating novel AFM sensors for simultaneous lateral and vertical force measurement and on developing a new original approach to increase the time resolution in AFM measurements. Due to the fundamental nature of this work we expect the long term impact of this work to be in surface science, chemistry, molecular electronics and life sciences. In the short term we expect to develop the AFM into a practical tool for chemical structure determination of unknown molecules and we will employ atomic manipulation and high resolution AFM imaging to image, modify and functionalize graphene edge structures with atomic scale precision with the prospect of exploring and developing novel molecular devices.

The objective of this project is to advance and use Atomic Force Microscopy (AFM) to explore the physical and chemical properties of single molecules and molecular systems with unprecedented spatial resolution. We will use AFM to develop atomically resolved molecular imaging with structural and chemical identification and investigate charge distribution and transfer in molecular systems. The AFM will allow the extension of seminal Scanning Tunneling Microscopy (STM) work on atoms/molecules on ultra-thin insulating films to thick insulating films, to control and explore single molecule chemistry processes in utmost detail. The whole work will be significantly based on the development and exploitation of novel atomic and molecular manipulation processes to control matter at the atomic scale, both for fabricating novel complex molecular nanostructures with atomic scale precision and understanding these systems, as well as for probe-tip functionalization to tailor tip-substrate interaction. Instrumental enhancements will focus on fabricating novel AFM sensors for simultaneous lateral and vertical force measurement and on developing a new original approach to increase the time resolution in AFM measurements. Due to the fundamental nature of this work we expect the long term impact of this work to be in surface science, chemistry, molecular electronics and life sciences. In the short term we expect to develop the AFM into a practical tool for chemical structure determination of unknown molecules and we will employ atomic manipulation and high resolution AFM imaging to image, modify and functionalize graphene edge structures with atomic scale precision with the prospect of exploring and developing novel molecular devices.

Max ERC Funding

2 496 720 €

Duration

Start date: 2011-12-01, End date: 2016-11-30

Project acronymCFRFSS

ProjectChromatin Fiber and Remodeling Factor Structural Studies

Researcher (PI)Timothy John Richmond

Host Institution (HI)EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Call DetailsAdvanced Grant (AdG), LS1, ERC-2012-ADG_20120314

Summary"DNA in higher organisms is organized in a nucleoprotein complex called chromatin. The structure of chromatin is responsible for compacting DNA to fit within the nucleus and for governing its access in nuclear processes. Epigenetic information is encoded chiefly via chromatin modifications. Readout of the genetic code depends on chromatin remodeling, a process actively altering chromatin structure. An understanding of the hierarchical structure of chromatin and of structurally based, remodeling mechanisms will have enormous impact for developments in medicine.
Following our high resolution structure of the nucleosome core particle, the fundamental repeating unit of chromatin, we have endeavored to determine the structure of the chromatin fiber. We showed with our X-ray structure of a tetranucleosome how nucleosomes could be organized in the fiber. Further progress has been limited by structural polymorphism and crystal disorder, but new evidence on the in vivo spacing of nucleosomes in chromatin should stimulate more advances. Part A of this application describes how we would apply these new findings to our cryo-electron microscopy study of the chromatin fiber and to our crystallographic study of a tetranucleosome containing linker histone.
Recently, my laboratory succeeded in providing the first structurally based mechanism for nucleosome spacing by a chromatin remodeling factor. We combined the X-ray structure of ISW1a(ATPase) bound to DNA with cryo-EM structures of the factor bound to two different nucleosomes to build a model showing how this remodeler uses a dinucleosome, not a mononucleosome, as its substrate. Our results from a functional assay using ISW1a further justified this model. Part B of this application describes how we would proceed to the relevant cryo-EM and X-ray structures incorporating dinucleosomes. Our recombinant ISW1a allows us to study in addition the interaction of the ATPase domain with nucleosome substrates."

"DNA in higher organisms is organized in a nucleoprotein complex called chromatin. The structure of chromatin is responsible for compacting DNA to fit within the nucleus and for governing its access in nuclear processes. Epigenetic information is encoded chiefly via chromatin modifications. Readout of the genetic code depends on chromatin remodeling, a process actively altering chromatin structure. An understanding of the hierarchical structure of chromatin and of structurally based, remodeling mechanisms will have enormous impact for developments in medicine.
Following our high resolution structure of the nucleosome core particle, the fundamental repeating unit of chromatin, we have endeavored to determine the structure of the chromatin fiber. We showed with our X-ray structure of a tetranucleosome how nucleosomes could be organized in the fiber. Further progress has been limited by structural polymorphism and crystal disorder, but new evidence on the in vivo spacing of nucleosomes in chromatin should stimulate more advances. Part A of this application describes how we would apply these new findings to our cryo-electron microscopy study of the chromatin fiber and to our crystallographic study of a tetranucleosome containing linker histone.
Recently, my laboratory succeeded in providing the first structurally based mechanism for nucleosome spacing by a chromatin remodeling factor. We combined the X-ray structure of ISW1a(ATPase) bound to DNA with cryo-EM structures of the factor bound to two different nucleosomes to build a model showing how this remodeler uses a dinucleosome, not a mononucleosome, as its substrate. Our results from a functional assay using ISW1a further justified this model. Part B of this application describes how we would proceed to the relevant cryo-EM and X-ray structures incorporating dinucleosomes. Our recombinant ISW1a allows us to study in addition the interaction of the ATPase domain with nucleosome substrates."

SummarySpecificity in the ubiquitin-proteasome system is largely conferred by ubiquitin E3 ligases (E3s). Cullin-RING ligases (CRLs), constituting ~30% of all E3s in humans, mediate the ubiquitination of ~20% of the proteins degraded by the proteasome. CRLs are divided into seven families based on their cullin constituent. Each cullin binds a RING domain protein, and a vast repertoire of adaptor/substrate receptor modules, collectively creating more than 200 distinct CRLs. All CRLs are regulated by the COP9 signalosome (CSN), an eight-protein isopeptidase that removes the covalently attached activator, NEDD8, from the cullin. Independent of NEDD8 cleavage, CSN forms protective complexes with CRLs, which prevents destructive auto-ubiquitination.
The integrity of the CSN-CRL system is crucially important for the normal cell physiology. Based on our previous work on CRL structures (Fischer, et al., Nature 2014; Fischer, et al., Cell 2011) and that of isolated CSN (Lingaraju et al., Nature 2014), We now intend to provide the underlying molecular mechanism of CRL regulation by CSN. Structural insights at atomic resolution, combined with in vitro and in vivo functional studies are designed to reveal (i) how the signalosome deneddylates and maintains the bound ligases in an inactive state, (ii) how the multiple CSN subunits bind to structurally diverse CRLs, and (iii) how CSN is itself subject to regulation by post-translational modifications or additional further factors.
The ERC funding would allow my lab to pursue an ambitious interdisciplinary approach combining X-ray crystallography, cryo-electron microscopy, biochemistry and cell biology. This is expected to provide a unique molecular understanding of CSN action. Beyond ubiquitination, insight into this >13- subunit CSN-CRL assembly will allow examining general principles of multi-subunit complex action and reveal how the numerous, often essential, subunits contribute to complex function.

Specificity in the ubiquitin-proteasome system is largely conferred by ubiquitin E3 ligases (E3s). Cullin-RING ligases (CRLs), constituting ~30% of all E3s in humans, mediate the ubiquitination of ~20% of the proteins degraded by the proteasome. CRLs are divided into seven families based on their cullin constituent. Each cullin binds a RING domain protein, and a vast repertoire of adaptor/substrate receptor modules, collectively creating more than 200 distinct CRLs. All CRLs are regulated by the COP9 signalosome (CSN), an eight-protein isopeptidase that removes the covalently attached activator, NEDD8, from the cullin. Independent of NEDD8 cleavage, CSN forms protective complexes with CRLs, which prevents destructive auto-ubiquitination.
The integrity of the CSN-CRL system is crucially important for the normal cell physiology. Based on our previous work on CRL structures (Fischer, et al., Nature 2014; Fischer, et al., Cell 2011) and that of isolated CSN (Lingaraju et al., Nature 2014), We now intend to provide the underlying molecular mechanism of CRL regulation by CSN. Structural insights at atomic resolution, combined with in vitro and in vivo functional studies are designed to reveal (i) how the signalosome deneddylates and maintains the bound ligases in an inactive state, (ii) how the multiple CSN subunits bind to structurally diverse CRLs, and (iii) how CSN is itself subject to regulation by post-translational modifications or additional further factors.
The ERC funding would allow my lab to pursue an ambitious interdisciplinary approach combining X-ray crystallography, cryo-electron microscopy, biochemistry and cell biology. This is expected to provide a unique molecular understanding of CSN action. Beyond ubiquitination, insight into this >13- subunit CSN-CRL assembly will allow examining general principles of multi-subunit complex action and reveal how the numerous, often essential, subunits contribute to complex function.

SummaryMovement is the behavioral output of the nervous system. Animals carry out an enormous repertoire of distinct actions, spanning from seemingly simple repetitive tasks like walking to much more complex movements such as forelimb manipulation tasks. An important question is how neuronal circuits are organized and function to choose, maintain, adjust and terminate these many distinct motor behaviors. Recent technological advances in neuroscience have made it possible to begin to unravel the links between the organization of specific neuronal circuit elements in the CNS and the control of movement, a topic that will be central to this research program.
While past work proposes that supraspinal centers in the brainstem are instrumental to the control of action diversification, little is known about how brainstem circuits translate movement intention to body control, how competing motor programs are selected, and how behavioral state influences movement control. The goal of this research project is to unravel the circuit blueprint of mouse descending motor pathways at a fine-scale level and to probe the intersection between revealed circuit organization and their behavioral function at many levels. The focus will be on studies on the interactions between brainstem neurons and spinal circuits to determine how initiation, duration, termination and selection of motor programs are implemented through specific neuronal subpopulations. Mapping descending connectivity matrices of motor circuits will serve as entry point and we will make use of state-of-the art intersectional technology including mouse genetics, viral approaches, in vivo neuronal recordings and activity manipulations of specific neuronal populations during behavior. Together, our project will elucidate the circuit organization and function of the descending motor output system and thereby uncover principles of how the nervous system generates diverse actions.

Movement is the behavioral output of the nervous system. Animals carry out an enormous repertoire of distinct actions, spanning from seemingly simple repetitive tasks like walking to much more complex movements such as forelimb manipulation tasks. An important question is how neuronal circuits are organized and function to choose, maintain, adjust and terminate these many distinct motor behaviors. Recent technological advances in neuroscience have made it possible to begin to unravel the links between the organization of specific neuronal circuit elements in the CNS and the control of movement, a topic that will be central to this research program.
While past work proposes that supraspinal centers in the brainstem are instrumental to the control of action diversification, little is known about how brainstem circuits translate movement intention to body control, how competing motor programs are selected, and how behavioral state influences movement control. The goal of this research project is to unravel the circuit blueprint of mouse descending motor pathways at a fine-scale level and to probe the intersection between revealed circuit organization and their behavioral function at many levels. The focus will be on studies on the interactions between brainstem neurons and spinal circuits to determine how initiation, duration, termination and selection of motor programs are implemented through specific neuronal subpopulations. Mapping descending connectivity matrices of motor circuits will serve as entry point and we will make use of state-of-the art intersectional technology including mouse genetics, viral approaches, in vivo neuronal recordings and activity manipulations of specific neuronal populations during behavior. Together, our project will elucidate the circuit organization and function of the descending motor output system and thereby uncover principles of how the nervous system generates diverse actions.

Max ERC Funding

2 500 000 €

Duration

Start date: 2016-09-01, End date: 2021-08-31

Project acronymDHISP

ProjectDorsal Horn Interneurons in Sensory Processing

Researcher (PI)Hanns Ulrich Zeilhofer

Host Institution (HI)UNIVERSITAT ZURICH

Call DetailsAdvanced Grant (AdG), LS5, ERC-2009-AdG

SummaryChronic pain syndromes are to a large extent due to maladaptive plastic changes in the CNS. A CNS area particularly relevant for such changes is the spinal dorsal horn, where inputs from nociceptive and non-nociceptive fibers undergo their first synaptic integration. This area harbors a sophisticated network of interneurons, which function as a gate-control unit for incoming sensory signals. Several different types of interneurons can be distinguished based e.g. on their neurotransmitter and neuropeptide content. Despite more than 40 years of research, our knowledge about the integration of these neurons in dorsal horn circuits and their contribution to sensory processing is still very limited. This proposal aims at a comprehensive characterization of the dorsal horn neuronal network under normal conditions and in chronic pain states with a focus on inhibitory interneurons. A genome-wide analysis of the gene expression profile shall be made from defined dorsal horn interneurons genetically tagged with fluorescent markers and isolated by fluorescence activated cell sorting. A functional characterization of the connectivity of these neurons in spinal cord slices and of their role in in vivo sensory processing shall be achieved with optogenetic tools (channelrhodopsin-2), which permit activation of these neurons with light. Finally, behavioral analyses shall be made in mice after diphteria toxin-mediated ablation of defined interneuron types. All three approaches shall be applied to naïve mice and to mice with inflammatory or neuropathic pain. The results from these studies will improve our understanding of the malfunctioning of sensory processing in chronic pain states and will provide the basis for novel approaches to the prevention or reversal of chronic pain states.

Chronic pain syndromes are to a large extent due to maladaptive plastic changes in the CNS. A CNS area particularly relevant for such changes is the spinal dorsal horn, where inputs from nociceptive and non-nociceptive fibers undergo their first synaptic integration. This area harbors a sophisticated network of interneurons, which function as a gate-control unit for incoming sensory signals. Several different types of interneurons can be distinguished based e.g. on their neurotransmitter and neuropeptide content. Despite more than 40 years of research, our knowledge about the integration of these neurons in dorsal horn circuits and their contribution to sensory processing is still very limited. This proposal aims at a comprehensive characterization of the dorsal horn neuronal network under normal conditions and in chronic pain states with a focus on inhibitory interneurons. A genome-wide analysis of the gene expression profile shall be made from defined dorsal horn interneurons genetically tagged with fluorescent markers and isolated by fluorescence activated cell sorting. A functional characterization of the connectivity of these neurons in spinal cord slices and of their role in in vivo sensory processing shall be achieved with optogenetic tools (channelrhodopsin-2), which permit activation of these neurons with light. Finally, behavioral analyses shall be made in mice after diphteria toxin-mediated ablation of defined interneuron types. All three approaches shall be applied to naïve mice and to mice with inflammatory or neuropathic pain. The results from these studies will improve our understanding of the malfunctioning of sensory processing in chronic pain states and will provide the basis for novel approaches to the prevention or reversal of chronic pain states.

Max ERC Funding

2 467 000 €

Duration

Start date: 2010-05-01, End date: 2016-04-30

Project acronymEUKARYOTIC RIBOSOME

ProjectStructural studies of the eukaryotic ribosome by X-ray crystallography

Researcher (PI)Nenad Ban

Host Institution (HI)EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Call DetailsAdvanced Grant (AdG), LS1, ERC-2009-AdG

SummaryThe ribosome is a large cellular organelle that plays a central role in the process of protein synthesis in all organisms. Currently, structural information at atomic resolution exists only for bacterial ribosomes and some of their functional complexes. Eukaryotic ribosomes are larger and significantly more complex than their bacterial counterparts. They consist of two unequal subunits with a combined molecular weight of approximately 4 million Daltons and contain 70-80 different protein molecules and four different RNAs. Currently the only structural information on eukaryotic ribosomes is available from cryo electron microscopic reconstructions in the nanometer resolution range, which is insufficient to derive information about the function of the eukaryotic ribosome at the atomic level. The aim of this proposal is to use X-ray crystallography to obtain structural and functional information on the eukaryotic ribosome and its functional complexes at high resolution. The key targets of the structural work will be: i) the structure of the small ribosomal subunit, ii) the structure of the large ribosomal subunit, and iii) structures of complexes involved in the initiation of protein synthesis. Besides the obvious fundamental importance of this research for understanding protein synthesis in eukaryotes the proposed studies will also be the prerequisite for understanding the structural basis of the regulation of protein synthesis in normal cells and how it is perturbed in various diseases. Finally, comparing the structures of bacterial and eukaryotic ribosomes is important for understanding the specificity of various clinically used antibiotics for the bacterial ribosome.

The ribosome is a large cellular organelle that plays a central role in the process of protein synthesis in all organisms. Currently, structural information at atomic resolution exists only for bacterial ribosomes and some of their functional complexes. Eukaryotic ribosomes are larger and significantly more complex than their bacterial counterparts. They consist of two unequal subunits with a combined molecular weight of approximately 4 million Daltons and contain 70-80 different protein molecules and four different RNAs. Currently the only structural information on eukaryotic ribosomes is available from cryo electron microscopic reconstructions in the nanometer resolution range, which is insufficient to derive information about the function of the eukaryotic ribosome at the atomic level. The aim of this proposal is to use X-ray crystallography to obtain structural and functional information on the eukaryotic ribosome and its functional complexes at high resolution. The key targets of the structural work will be: i) the structure of the small ribosomal subunit, ii) the structure of the large ribosomal subunit, and iii) structures of complexes involved in the initiation of protein synthesis. Besides the obvious fundamental importance of this research for understanding protein synthesis in eukaryotes the proposed studies will also be the prerequisite for understanding the structural basis of the regulation of protein synthesis in normal cells and how it is perturbed in various diseases. Finally, comparing the structures of bacterial and eukaryotic ribosomes is important for understanding the specificity of various clinically used antibiotics for the bacterial ribosome.

SummaryThe quest for mechanical oscillators with ultralow dissipation is motivated by classical and quantum sensing and technology, and precision measurements. For decades, the most coherent mechanical oscillators were acoustic vibrations in kg-scale crystalline bars. Recently a paradigm shift has occurred. The combination of elastic strain engineering – a technique used in microelectronics – with phononic mode engineering has resulted in 1D nano-strings with a mechanical quality factor Q of 0.8 billion – the highest ever achieved at room temperature. Remarkably, these new techniques have major untapped potential, as they have only been applied to non-crystalline materials in 1D. We propose a new generation of strain-engineered crystalline and superconducting mechanical oscillators whose Q-factors are predicted to exceed 100 billion in up to 2 dimensions. We will seek to reach this theoretical limit, probe new dissipation mechanisms, and utilize these oscillators for quantum optomechanics in new regimes and achieve room temperature ground state cooling and ponderomotive squeezing. Likewise, we will apply these techniques to create highly coherent superconducting electromechanical devices at milli-Kelvin temperatures, enabling quantum-enhanced force sensing and 1 second decoherence times. Secondly, we will explore a fundamentally new method for measurement and manipulation of microwave fields with optical fields – the nascent field of circuit Cavity-Electro-Optics (cCEO). First recognized over a decade ago, it is possible with optical fields to cool, amplify or interferometrically read out microwaves. Yet to date this regime has remained in accessible due to insufficient coupling strength between the microwave and optical fields. We will overcome this challenge based on a new circuit architecture, allowing laser cooling and laser amplification of microwaves and electro-optical masing using optical backaction, and thereby opening an entirely new way to manipulate microwaves.

The quest for mechanical oscillators with ultralow dissipation is motivated by classical and quantum sensing and technology, and precision measurements. For decades, the most coherent mechanical oscillators were acoustic vibrations in kg-scale crystalline bars. Recently a paradigm shift has occurred. The combination of elastic strain engineering – a technique used in microelectronics – with phononic mode engineering has resulted in 1D nano-strings with a mechanical quality factor Q of 0.8 billion – the highest ever achieved at room temperature. Remarkably, these new techniques have major untapped potential, as they have only been applied to non-crystalline materials in 1D. We propose a new generation of strain-engineered crystalline and superconducting mechanical oscillators whose Q-factors are predicted to exceed 100 billion in up to 2 dimensions. We will seek to reach this theoretical limit, probe new dissipation mechanisms, and utilize these oscillators for quantum optomechanics in new regimes and achieve room temperature ground state cooling and ponderomotive squeezing. Likewise, we will apply these techniques to create highly coherent superconducting electromechanical devices at milli-Kelvin temperatures, enabling quantum-enhanced force sensing and 1 second decoherence times. Secondly, we will explore a fundamentally new method for measurement and manipulation of microwave fields with optical fields – the nascent field of circuit Cavity-Electro-Optics (cCEO). First recognized over a decade ago, it is possible with optical fields to cool, amplify or interferometrically read out microwaves. Yet to date this regime has remained in accessible due to insufficient coupling strength between the microwave and optical fields. We will overcome this challenge based on a new circuit architecture, allowing laser cooling and laser amplification of microwaves and electro-optical masing using optical backaction, and thereby opening an entirely new way to manipulate microwaves.

Max ERC Funding

2 496 000 €

Duration

Start date: 2019-10-01, End date: 2024-09-30

Project acronymFFlowCCS

ProjectFluid Flow in Complex and Curved Spaces

Researcher (PI)Hans Jürgen Herrmann

Host Institution (HI)EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Call DetailsAdvanced Grant (AdG), PE3, ERC-2012-ADG_20120216

SummaryIn many natural and industrial situations, fluids in cavities, membranes or pipes of complex shape grow as well as modify the structures through which they flow. This leads to important challenges both fundamental, like biological morphogenesis, and practical, like the motion of nano-electromechanical systems (NEMS). We seek to substantially advance the understanding of the resulting shapes and instabilities. Our approach will focus on numerical methods, validated through theoretical and experimental analysis.
Mathematically fluid-structure interactions involve ambitious moving boundary problems, where structure and fluid flow feedback on one another in complex ways. Detailed analysis requires precise modeling of coupling between very strongly de¬forming elasto-plastic solids and fluid flow in intricately curved spaces and solving both iteratively many times. To address this computational challenge, significant innovations will be implemented, including the use of novel erosion laws, the insertion of spatial curvature and metric directly into the equations of motion of the fluid, and special methods to handle the singular behaviour at kinks and constrictions. Our fluid solvers will be new variants of Lattice Boltzmann Models (LBM) coupled to temperature and concentration fields. The accuracy of the methods will be quantitatively validated by experiments.
An unconventional hydrodynamic formulation for electronic currents will provide big advantages. We will develop LBM solvers for quantum and relativistic fluids and in particular create a Lattice Wigner model and couple it to the molecular dynamics of the support.
Our method will open new horizons for the design of continuously regenerating filters, for shape optimi¬zation of heat exchangers and catalysts and for the engineering of electronic devices. Our approach will also shed light on sand avalanches in oil extraction, on aspects of folding in living matter, and on electromechanical instabilities.

In many natural and industrial situations, fluids in cavities, membranes or pipes of complex shape grow as well as modify the structures through which they flow. This leads to important challenges both fundamental, like biological morphogenesis, and practical, like the motion of nano-electromechanical systems (NEMS). We seek to substantially advance the understanding of the resulting shapes and instabilities. Our approach will focus on numerical methods, validated through theoretical and experimental analysis.
Mathematically fluid-structure interactions involve ambitious moving boundary problems, where structure and fluid flow feedback on one another in complex ways. Detailed analysis requires precise modeling of coupling between very strongly de¬forming elasto-plastic solids and fluid flow in intricately curved spaces and solving both iteratively many times. To address this computational challenge, significant innovations will be implemented, including the use of novel erosion laws, the insertion of spatial curvature and metric directly into the equations of motion of the fluid, and special methods to handle the singular behaviour at kinks and constrictions. Our fluid solvers will be new variants of Lattice Boltzmann Models (LBM) coupled to temperature and concentration fields. The accuracy of the methods will be quantitatively validated by experiments.
An unconventional hydrodynamic formulation for electronic currents will provide big advantages. We will develop LBM solvers for quantum and relativistic fluids and in particular create a Lattice Wigner model and couple it to the molecular dynamics of the support.
Our method will open new horizons for the design of continuously regenerating filters, for shape optimi¬zation of heat exchangers and catalysts and for the engineering of electronic devices. Our approach will also shed light on sand avalanches in oil extraction, on aspects of folding in living matter, and on electromechanical instabilities.

Max ERC Funding

2 200 000 €

Duration

Start date: 2013-01-01, End date: 2017-12-31

Project acronymINSEETO

ProjectIn-situ second harmonic generation for emergent electronics in transition-metal oxides

Researcher (PI)Manfred FIEBIG

Host Institution (HI)EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Call DetailsAdvanced Grant (AdG), PE3, ERC-2015-AdG

SummarySince transition-metal oxides heterostructures can be grown by pulsed laser deposition (PLD) with semiconductor-like accuracy, fascinating phases and functionalities derived from their spin-charge correlations have been discovered. So far, reflection high-energy electron diffraction is the only widely established technique for monitoring the structure and homogeneity of multilayers in-situ, while they are growing, and provide direct feedback information on how to optimise the growth process. With our proposal we will introduce second harmonic generation (SHG) as new in-situ technique that allows us to track spin-and charge-related phenomena such as ferroelectricity, (anti-) ferromagnetism, insulator-metal transitions, domain coupling effects or interface states in a non-invasive way throughout the deposition process. With this we are pursuing two goals: first, to establish SHG as new in-situ characterization technique in PLD which monitors strong spin-charge correlation effects while they emerge during growth; second, to apply in-situ SHG for tailoring novel functionalities in exemplary chosen types of transition-metal-oxide heterostructures of great current interest. These model systems are (i) proper ferroelectrics tuned to high-k dielectric response and improper ferroelectrics whose behaviour is determined by the unusual nature of the polar state; (ii) compounds in which the interplay of strain and defects leads to novel and reversibly tuneable states of matter; (iii) heterostructures with functionalities originating from the interaction across interfaces. In-situ SHG as new, property-monitoring tool in PLD has an immense potential to uncover new states of matter and functionalities. We are convinced that this will play an essential role in the leap towards the next generation of functional oxide heterostructures.

Since transition-metal oxides heterostructures can be grown by pulsed laser deposition (PLD) with semiconductor-like accuracy, fascinating phases and functionalities derived from their spin-charge correlations have been discovered. So far, reflection high-energy electron diffraction is the only widely established technique for monitoring the structure and homogeneity of multilayers in-situ, while they are growing, and provide direct feedback information on how to optimise the growth process. With our proposal we will introduce second harmonic generation (SHG) as new in-situ technique that allows us to track spin-and charge-related phenomena such as ferroelectricity, (anti-) ferromagnetism, insulator-metal transitions, domain coupling effects or interface states in a non-invasive way throughout the deposition process. With this we are pursuing two goals: first, to establish SHG as new in-situ characterization technique in PLD which monitors strong spin-charge correlation effects while they emerge during growth; second, to apply in-situ SHG for tailoring novel functionalities in exemplary chosen types of transition-metal-oxide heterostructures of great current interest. These model systems are (i) proper ferroelectrics tuned to high-k dielectric response and improper ferroelectrics whose behaviour is determined by the unusual nature of the polar state; (ii) compounds in which the interplay of strain and defects leads to novel and reversibly tuneable states of matter; (iii) heterostructures with functionalities originating from the interaction across interfaces. In-situ SHG as new, property-monitoring tool in PLD has an immense potential to uncover new states of matter and functionalities. We are convinced that this will play an essential role in the leap towards the next generation of functional oxide heterostructures.

Summaryature has developed photosynthesis to power life. Networks of light harvesting antennas capture the sunlight to funnel the photonic energy towards reaction centres. Surprisingly, quantum coherences are observed in the energy transfer of photosynthetic complexes, even at room temperature.
Does nature exploit quantum concepts? Does the coherence help to find an optimal path for robust or efficient transfer? How are the coherences sustained? What is their spatial extent in a real light-harvesting network? So far only solutions of complexes were studied, far from the natural network operation, putting on hold conclusions as to a biological role of the coherences.
My group recently succeeded in the first detection of coherent oscillations of a single photo-synthetic complex at physiological conditions, and non-classical photon emission of individual complexes. These pioneering results, together with our expertise in nanophotonics, pave the way to address photosynthetic networks in real nano-space and on femtosecond timescale. Specific objectives are:
--Ultrafast single protein detection: tracing the fs coherent energy transfer path of an individual complex; addressing the very nature of the persistent coherences.
-Beyond fluorescence: light harvesting complex are designed for light transport, not emission. I will explore innovative alternatives: optical antennas to enhance quantum efficiency; detection of stimulated emission; and electrical read-out on graphene.
-Nanoscale light transport: using local excitation and detection by nanoholes, nanoslits and scanning antenna probes I will spatially map the extent of the inter-complex transfer.
-The network: combining both coherent fs excitation and localized nanoscale excitation/detection I will track the extent of coherences throughout the network.
The impact of this first exploration of light transport in a nanoscale bionetwork ranges to solar energy management, molecular biology, polymer chemistry and material science.

ature has developed photosynthesis to power life. Networks of light harvesting antennas capture the sunlight to funnel the photonic energy towards reaction centres. Surprisingly, quantum coherences are observed in the energy transfer of photosynthetic complexes, even at room temperature.
Does nature exploit quantum concepts? Does the coherence help to find an optimal path for robust or efficient transfer? How are the coherences sustained? What is their spatial extent in a real light-harvesting network? So far only solutions of complexes were studied, far from the natural network operation, putting on hold conclusions as to a biological role of the coherences.
My group recently succeeded in the first detection of coherent oscillations of a single photo-synthetic complex at physiological conditions, and non-classical photon emission of individual complexes. These pioneering results, together with our expertise in nanophotonics, pave the way to address photosynthetic networks in real nano-space and on femtosecond timescale. Specific objectives are:
--Ultrafast single protein detection: tracing the fs coherent energy transfer path of an individual complex; addressing the very nature of the persistent coherences.
-Beyond fluorescence: light harvesting complex are designed for light transport, not emission. I will explore innovative alternatives: optical antennas to enhance quantum efficiency; detection of stimulated emission; and electrical read-out on graphene.
-Nanoscale light transport: using local excitation and detection by nanoholes, nanoslits and scanning antenna probes I will spatially map the extent of the inter-complex transfer.
-The network: combining both coherent fs excitation and localized nanoscale excitation/detection I will track the extent of coherences throughout the network.
The impact of this first exploration of light transport in a nanoscale bionetwork ranges to solar energy management, molecular biology, polymer chemistry and material science.

SummaryAlternative splicing of messenger RNA precursors is a prevalent form of gene regulation that greatly expands the coding capacity and regulatory opportunities of higher eukaryotic genomes. It contributes to cell differentiation and pluripotency and its deregulation promotes cancer progression, as evidenced by the frequent occurrence of cancer-associated mutations in splicing factors, which are also targets of anti-tumor drugs. Despite its prevalence and relevance, the underlying mechanisms of regulation remain poorly understood. This proposal aims to develop and apply systematic approaches that can allow us to carry out the equivalent of genetic analysis of splicing regulation in cancer and pluripotent cells. These technologies can help to unweave the complex network of functional interactions within the spliceosome and of the spliceosome with regulatory factors, exhaustively map the contribution of regulatory sequences and be used to investigate, with unprecedented detail, mechanisms of regulation for essentially any regulator or alternative splicing event operating in a particular cell line. Such approaches can offer a unique opportunity to address key unresolved mechanistic questions, including the molecular basis for positional effects of splicing regulatory factors (RNA Maps), the regulatory potential of the core spliceosome and the integration of alternative splicing with other cell regulatory programs. We will combine these approaches with biochemical and cellular assays to investigate detailed mechanisms of regulation relevant for the control of cell proliferation and/or pluripotency in cancer and induced pluripotent stem (iPS) cells. Progress in this area can contribute to reveal the molecular logic governing a key layer of gene regulation and has the potential to discover novel factors and regulatory circuits that trigger or modulate cell growth, differentiation and cancer progression.

Alternative splicing of messenger RNA precursors is a prevalent form of gene regulation that greatly expands the coding capacity and regulatory opportunities of higher eukaryotic genomes. It contributes to cell differentiation and pluripotency and its deregulation promotes cancer progression, as evidenced by the frequent occurrence of cancer-associated mutations in splicing factors, which are also targets of anti-tumor drugs. Despite its prevalence and relevance, the underlying mechanisms of regulation remain poorly understood. This proposal aims to develop and apply systematic approaches that can allow us to carry out the equivalent of genetic analysis of splicing regulation in cancer and pluripotent cells. These technologies can help to unweave the complex network of functional interactions within the spliceosome and of the spliceosome with regulatory factors, exhaustively map the contribution of regulatory sequences and be used to investigate, with unprecedented detail, mechanisms of regulation for essentially any regulator or alternative splicing event operating in a particular cell line. Such approaches can offer a unique opportunity to address key unresolved mechanistic questions, including the molecular basis for positional effects of splicing regulatory factors (RNA Maps), the regulatory potential of the core spliceosome and the integration of alternative splicing with other cell regulatory programs. We will combine these approaches with biochemical and cellular assays to investigate detailed mechanisms of regulation relevant for the control of cell proliferation and/or pluripotency in cancer and induced pluripotent stem (iPS) cells. Progress in this area can contribute to reveal the molecular logic governing a key layer of gene regulation and has the potential to discover novel factors and regulatory circuits that trigger or modulate cell growth, differentiation and cancer progression.

Max ERC Funding

2 159 574 €

Duration

Start date: 2015-10-01, End date: 2021-03-31

Project acronymMCircuits

ProjectConnectivity, plasticity and function of an olfactory memory circuit

SummaryThe brain accumulates knowledge by experience-driven modifications of neuronal connectivity and creates models of the world that enable intelligent behavior. It is thought that these processes are based on autoassociative mechanisms of circuit plasticity. However, direct tests of these fundamental concepts are difficult because they require dense reconstructions of neuronal wiring diagrams. We will dissect structural and functional mechanisms of autoassociative memory in telencephalic area Dp of adult zebrafish, the homologue of olfactory cortex. The small size of the zebrafish brain provides essential advantages for exhaustive measurements of neuronal activity and connectivity patterns. Key predictions of theoretical models will be examined by analyzing effects of odor discrimination learning on the dynamics and stability of odor representations in Dp. The underlying structural circuit modifications will be examined in the same brains by circuit reconstruction using serial block face scanning electron microscopy (SBEM). The dense reconstruction of neuronal ensembles responding to learned and novel odors will allow for advanced analyses of structure-function relationships that have not been possible so far. Odor stimulation in a virtual environment will be combined with optogenetic activation or silencing of neuromodulatory inputs to write and disrupt specific olfactory memories and to analyze the effects on behavior and connectivity. The underlying cellular mechanisms of synaptic plasticity and metaplasticity will be examined by electrophysiology, imaging and optogenetic approaches. Mutants will be used to assess effects of disease-related mutations on circuit structure, function and plasticity. These mechanistic analyses are guided by theoretical models, expected to generate direct insights into elementary computations underlying higher brain functions, and likely to uncover causal links between circuit connectivity, circuit function and behavior.

The brain accumulates knowledge by experience-driven modifications of neuronal connectivity and creates models of the world that enable intelligent behavior. It is thought that these processes are based on autoassociative mechanisms of circuit plasticity. However, direct tests of these fundamental concepts are difficult because they require dense reconstructions of neuronal wiring diagrams. We will dissect structural and functional mechanisms of autoassociative memory in telencephalic area Dp of adult zebrafish, the homologue of olfactory cortex. The small size of the zebrafish brain provides essential advantages for exhaustive measurements of neuronal activity and connectivity patterns. Key predictions of theoretical models will be examined by analyzing effects of odor discrimination learning on the dynamics and stability of odor representations in Dp. The underlying structural circuit modifications will be examined in the same brains by circuit reconstruction using serial block face scanning electron microscopy (SBEM). The dense reconstruction of neuronal ensembles responding to learned and novel odors will allow for advanced analyses of structure-function relationships that have not been possible so far. Odor stimulation in a virtual environment will be combined with optogenetic activation or silencing of neuromodulatory inputs to write and disrupt specific olfactory memories and to analyze the effects on behavior and connectivity. The underlying cellular mechanisms of synaptic plasticity and metaplasticity will be examined by electrophysiology, imaging and optogenetic approaches. Mutants will be used to assess effects of disease-related mutations on circuit structure, function and plasticity. These mechanistic analyses are guided by theoretical models, expected to generate direct insights into elementary computations underlying higher brain functions, and likely to uncover causal links between circuit connectivity, circuit function and behavior.

Max ERC Funding

2 495 839 €

Duration

Start date: 2017-10-01, End date: 2022-09-30

Project acronymMemoryDynamics

ProjectWriting and editing of memories from acquisition to long-term consolidation

SummaryNervous systems produce adaptive behavior, arguably their most important function, through learning and memory. Memories ensure that what is learned will be available for later retrieval. Upon the initial learning process, synaptic plasticity important for memory consolidation is triggered within minutes, but whether, and in which form memories will be retained more permanently can be influenced by information and insights gained after the initial trigger. Learning and memory have been studied extensively, but we still know very little about the mechanisms through which memories are shaped after acquisition. Here we hypothesize that instead of simply reflecting requirements to produce long-term memory traces, cascades of plasticity processes induced at the time of acquisition might also reflect systems requirements for updating of new relevant information, as well as selection of potentially useful memories that need to enter the process of long-term consolidation.
Recent advances in neuroscience have provided powerful novel means to reveal, analyze and manipulate memory traces in the living brain, from single neurons to systems, and to interrogate their function. This research program will address the functional roles of learning-related plasticity processes unfolding subsequent to acquisition in learning and memory. We will investigate how hippocampal memories are shaped during several hours after acquisition through network activity and addition of new information through experience, and how these processes involve unique roles for dorsal hippocampus, and for dedicated neuronal circuits. Furthermore, we will study how shaped memories are then long-term consolidated, including the key role of ventral hippocampal circuitry, and how memories are further modified through subsequent learning. This research will produce fundamentally novel insights into how learning leads to adaptive behavior through writing and editing of memories.

Nervous systems produce adaptive behavior, arguably their most important function, through learning and memory. Memories ensure that what is learned will be available for later retrieval. Upon the initial learning process, synaptic plasticity important for memory consolidation is triggered within minutes, but whether, and in which form memories will be retained more permanently can be influenced by information and insights gained after the initial trigger. Learning and memory have been studied extensively, but we still know very little about the mechanisms through which memories are shaped after acquisition. Here we hypothesize that instead of simply reflecting requirements to produce long-term memory traces, cascades of plasticity processes induced at the time of acquisition might also reflect systems requirements for updating of new relevant information, as well as selection of potentially useful memories that need to enter the process of long-term consolidation.
Recent advances in neuroscience have provided powerful novel means to reveal, analyze and manipulate memory traces in the living brain, from single neurons to systems, and to interrogate their function. This research program will address the functional roles of learning-related plasticity processes unfolding subsequent to acquisition in learning and memory. We will investigate how hippocampal memories are shaped during several hours after acquisition through network activity and addition of new information through experience, and how these processes involve unique roles for dorsal hippocampus, and for dedicated neuronal circuits. Furthermore, we will study how shaped memories are then long-term consolidated, including the key role of ventral hippocampal circuitry, and how memories are further modified through subsequent learning. This research will produce fundamentally novel insights into how learning leads to adaptive behavior through writing and editing of memories.

SummaryThe mesocorticolimbic (MCL) system, extending from the ventral tegmental area (VTA) to the nucleus accumbens and prefrontal cortex, comprises a dopamine (DA) projection implicated in reinforcement learning. The MCL system is the target of addictive substances and of drug-evoked synaptic plasticity, a cellular mechanism that may underlie the adaptive, pathological behaviors that occur after repeated drug exposure. While most previous work has focused on excitatory transmission, recent studies suggest that inhibitory transmission may play a crucial role in mediating specific functions of the MCL system. However the identity of the inhibitory synapses and circuits and the plasticity mechanisms underlying these forms of normal and pathological learning remain elusive.
We hypothesize that distinct inhibitory circuits in the MCL system mediate specific behaviors and that adaptive synaptic plasticity of these circuits are fundamental to both normal reward learning and addictive behaviors.
We will test this hypothesis using optogenetic projection targeting to characterize specific inhibitory projections, to selectively change the activity of these neurons in freely behaving animals to explore their behavioral relevance, and to identify precise circuit changes that underlie behavioral alterations after drug exposure. Taken together, the experiments we propose will not only identify the specific circuits and basic role of inhibition in mediating reward-related behaviors, but will allow us to understand how the alteration of these circuits after drugs can result in pathological behavior. Ultimately, our results will establish the importance of inhibitory synaptic transmission in the MCL system, are likely to fundamentally change current views of this important modulatory system, and will allow us to design strategies to interfere with drug-evoked synaptic plasticity to revert addictive behavior.

The mesocorticolimbic (MCL) system, extending from the ventral tegmental area (VTA) to the nucleus accumbens and prefrontal cortex, comprises a dopamine (DA) projection implicated in reinforcement learning. The MCL system is the target of addictive substances and of drug-evoked synaptic plasticity, a cellular mechanism that may underlie the adaptive, pathological behaviors that occur after repeated drug exposure. While most previous work has focused on excitatory transmission, recent studies suggest that inhibitory transmission may play a crucial role in mediating specific functions of the MCL system. However the identity of the inhibitory synapses and circuits and the plasticity mechanisms underlying these forms of normal and pathological learning remain elusive.
We hypothesize that distinct inhibitory circuits in the MCL system mediate specific behaviors and that adaptive synaptic plasticity of these circuits are fundamental to both normal reward learning and addictive behaviors.
We will test this hypothesis using optogenetic projection targeting to characterize specific inhibitory projections, to selectively change the activity of these neurons in freely behaving animals to explore their behavioral relevance, and to identify precise circuit changes that underlie behavioral alterations after drug exposure. Taken together, the experiments we propose will not only identify the specific circuits and basic role of inhibition in mediating reward-related behaviors, but will allow us to understand how the alteration of these circuits after drugs can result in pathological behavior. Ultimately, our results will establish the importance of inhibitory synaptic transmission in the MCL system, are likely to fundamentally change current views of this important modulatory system, and will allow us to design strategies to interfere with drug-evoked synaptic plasticity to revert addictive behavior.